Protein profile

VK055_1731

biotin synthase

Genome: KpATCC43816

Gene: bioB AIK80351.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GK97
Export view
Amino acids 338
Annotations 8
Features 26
PDB binders 16
Druggability 0.633

Overview

Basic information about this protein and its source genome.

Accession
VK055_1731
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
bioB AIK80351.1
Status
annotated
Amino acids
338
Structure source
AlphaFold + ColabFold
EC
2.8.1.6
GO
GO:0004076 Catalysis of the reaction: (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = [sulfur carrier]-H + biotin + 2 5'-deoxyadenosine + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin]. GO:0009102 The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
75.325
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
91.38

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.633
Structure A0A0H3GK97
Pocket Pocket 2
P2Rank 0.973
Structure A0A0H3GK97
Pocket Pocket 1
ColabFold model
FPocket 0.777 · Pocket 1
P2Rank 0.969 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 225 / 4744 genomes with a hit
Normalized 0.047

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0004076 Catalysis of the reaction: (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = [sulfur carrier]-H + biotin + 2 5'-deoxyadenosine + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin].
  • GO:0009102 The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0005506 Binding to an iron (Fe) ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
42 194 Pfam PF04055 Radical SAM superfamily
42 194 InterPro IPR007197 Radical SAM
2 305 Hamap MF_01694 Biotin synthase [bioB].
2 305 InterPro IPR002684 Biotin synthase/Biotin biosynthesis bifunctional protein BioAB
42 241 CDD cd01335 Radical_SAM
3 305 SUPERFAMILY SSF102114 Radical SAM enzymes
35 247 SMART SM00729 MiaB
35 247 InterPro IPR006638 Elp3/MiaA/NifB-like, radical SAM core domain
2 309 SFLD SFLDG01278 biotin synthase like
3 323 PANTHER PTHR22976 BIOTIN SYNTHASE
3 323 InterPro IPR002684 Biotin synthase/Biotin biosynthesis bifunctional protein BioAB
3 302 NCBIfam TIGR00433 biotin synthase BioB
3 302 InterPro IPR002684 Biotin synthase/Biotin biosynthesis bifunctional protein BioAB
1 311 PIRSF PIRSF001619 Biotin_synth
1 311 InterPro IPR024177 Biotin synthase
1 307 FunFam G3DSA:3.20.20.70:FF:000011 Biotin synthase
30 248 ProSiteProfiles PS51918 Radical SAM core domain profile.
30 248 InterPro IPR007197 Radical SAM
212 302 Pfam PF06968 Biotin and Thiamin Synthesis associated domain
212 302 InterPro IPR010722 Biotin and thiamin synthesis-associated domain
212 304 SMART SM00876 BATS_2
212 304 InterPro IPR010722 Biotin and thiamin synthesis-associated domain
1 307 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 307 InterPro IPR013785 Aldolase-type TIM barrel
2 309 SFLD SFLDF00272 biotin synthase
2 309 InterPro IPR024177 Biotin synthase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

Loading 3D structure...

Legend High Medium Low

Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GK97
AlphaFold — — full sequence — Viewing
ColabFold VK055_1731
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
2 0.633
3 0.003
1 0.001
12 0.0

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 54.47 0.973
2 2.92 0.075
3 2.61 0.061
4 2.38 0.051
5 1.67 0.023

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

66 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
1N7
4JXC
Q9X0Z6 631.9 Da LogP 2.20 TPSA 164.4 2 viol. ✓ Clean C[C@H](CCC(=O)NCCC[N+](C)(C)CC(CS(=O)(=O)O)O)[C…
41K
5FEP
Q9X0Z6 191.2 Da LogP -0.42 TPSA 86.6 ✓ Ro5 ✓ Clean C[C@]1(N[C@@H](CS1)C(=O)O)C(=O)O
5AD
3IIX
Q9X0Z6 251.2 Da LogP -0.95 TPSA 119.3 ✓ Ro5 ✓ Clean C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
5X8
5FEW
Q9X0Z6 370.4 Da LogP -1.83 TPSA 182.6 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
5XB
5FF2
Q9X0Z6 177.2 Da LogP -0.81 TPSA 86.6 ✓ Ro5 ✓ Clean C1[C@H](N[C@H](S1)C(=O)O)C(=O)O
5ZZ
5FF4
Q9X0Z6 219.3 Da LogP 0.36 TPSA 86.6 ✓ Ro5 ✓ Clean C[C@]1(N[C@@H](C(S1)(C)C)C(=O)O)C(=O)O
9SE
5FES
Q9X0Z6 238.1 Da LogP -1.03 TPSA 86.6 ✓ Ro5 ✓ Clean C[C@]1(N[C@@H](C[Se]1)C(=O)O)C(=O)O
CPS
3CIW
Q9X0Z6 614.9 Da LogP 2.88 TPSA 147.0 1 viol. ✓ Clean C[C@H](CCC(=O)NCCC[N+](C)(C)CCCS(=O)(=O)[O-])[C…
DTB
1R30
P12996 214.3 Da LogP 1.09 TPSA 78.4 ✓ Ro5 ✓ Clean C[C@H]1[C@H](NC(=O)N1)CCCCCC(=O)O
FES
1R30
P12996 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
MD0
3T7V
Q46E78 146.2 Da LogP -0.62 TPSA 89.3 ✓ Ro5 ✓ Clean C[C@H](CCN)[C@H](C(=O)O)N
PRS
5FF3
Q9X0Z6 133.2 Da LogP -0.27 TPSA 49.3 ✓ Ro5 ✓ Clean C1[C@H](NCS1)C(=O)O
SAT
3CIW
Q9X0Z6 140.1 Da LogP -1.04 TPSA 91.7 ✓ Ro5 ✓ Clean C(C(=O)O)S(=O)(=O)O
SE
5FF4
Q9X0Z6 81.0 Da LogP -0.92 TPSA 0.0 ✓ Ro5 ✓ Clean [SeH2]
SEC
5FEX
Q9X0Z6 168.1 Da LogP -1.28 TPSA 63.3 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)N)[SeH]
SFS
5FF4
Q9X0Z6 539.2 Da LogP -1.53 TPSA 0.0 1 viol. ✓ Clean [Fe]12[Se]3[Fe]4[Se]1[Fe]5[Se]2[Fe]3[Se]45

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.